Smooth cylinder after do kife cut?
I suppose you did a Boolean cut. That gets the job done fast, but you'll have a hard time cleaning up the mesh after the fact. You would be better off by first cutting a hole in the cylinder with the Knife Tool, taking care that the topology is correct (quads only). Then select, inset and push the polygons that form the perimeter of the hole inside the cylinder. After that, select the edges surrounding the newly formed hole and bevel them. After you apply the Subdivision Surface Modifier you should have a decent looking mesh.